StarGate Atlantis: Season Six
by Aengel
Summary: Six months after Atlantis' arrival to Earth, John Sheppard and the Atlantis Expedition are about to be thrust back into action.


******Episode 1-Friends and Enemies Part 1**

"Incoming wormhole!" the voice of Chief Master Sergeant Walter Harriman echoed over the base intercom. Major General Hank Landry, commander of Stargate Command, entered the embarkation room, flanked by the security response team that took up defensive positions around the ramp that led to the Stargate. The inner ring of the gate spun until seven chevrons locked into place. This triggered the activation of a wormhole behind the sealed iris.

Gen. Landry turned and looked up into the gate control room at Sergeant Harriman.

"Well Walter, who is it?"

"Receiving SG-2's IDC sir."

"They're late."

"Yes sir."

"Open the iris."

The iris was a trinium made barrier that dilates and retracts like a camera shutter to cover the exposed central part of the Stargate where wormholes connect. It is designed to keep out unwanted guests as it prevents matter form rematerializing through the wormhole. Each SG team, as well as various off world allies are given codes, called iris deactivation codes, which inform Stargate Command that they are friendly.

The iris contracted to reveal the bright blue, puddle-like, wormhole created by the stargate. Lt. Col. John Sheppard, commander of SG-2, was the first to emerge. His arrival generated ripples in the event horizon of the wormhole; the other three members of his team followed. Gen. Landry ordered the security teams to stand down as the stargate deactivated.

Sheppard unclipped the P-90 Personal Defense Weapon from the chest clip on his load bearing vest and handed it to the awaiting armorer at the end of the ramp.

"Welcome back SG-2." said Gen. Landry with his usual nod of approval.

"Thank you, sir." said Sheppard sharply.

"You're late colonel."

"Hopefully not too late sir, I was hoping to catch the USC game."

"I'm afraid you've missed the game Colonel, they lost."

"Damn, there goes twenty bucks."

Landry chuckled slightly, "Sorry Colonel. I can only hope the mission went smother than your betting choices?"

"The negotiations with the local farmers took longer than expected. Apparently, they trade their crops with the villages in exchange for medicine and they thought the villagers were holding out on them."

"I trust the situation was resolved then?"

"You could say that sir. The villagers refused to give up their best medicines to the farmers, but agreed to supply their usual assortment, along with the farmer's choice of a woman, for the winter season in exchange for crops."

"Where would the farmers of the galaxy be without you Col. Sheppard?"

"I had nothing to do with it sir, I simply suggested to the farmers that there might be something better than cutting edge medicines to exchange for."

"I'll be sure you get a glowing review in my report. Anyway, now that you're here you'll be happy to know that the _Daedalus_ has returned from its mission to the midway satellite and we've received a communique from our wraith friend. I want you in the briefing room as soon as you check in with Dr. Beckett."

This was music to Sheppard's ears. It had been six months since Atlantis arrived on Earth to stop a ZPM powered wraith hive ship form attacking the planet. The city suffered significant damage but when the repairs to Atlantis' shields and engines were complete the International Oversight Committee proposed to the president that the Pegasus galaxy be abandoned now that the city was on Earth; this put a stop to any return mission. Sheppard requested to lead an SG team so that he could continue to go off world. However, with the defeat of the Ori and the recent dissolution of the trust there was little action to be found in the Milky Way. As much as he feared that the wraith had found another way to Earth, he couldn't help but hope that something was happening that would require a return to Pegasus. He had unfinished business with the wraith, as did his team.

"Will due sir!" said Sheppard happily as he made his way to the infirmary.

The sound of bantos rods striking against each other filled the fitness room; Teyla Emmagan and Ronon Dex were engaging in a friendly sparring session. Bantos fighting was used by the Athosian people and utilizes one or two rods, or simply sticks. Since joining the Atlantis expedition Teyla had taught the style to many people, mainly Sheppard and Ronan, and led several practice sessions to keep her skills sharp.

No member of the expedition had quickly grasped bantos fighting as fast as Ronon Dex did. It's to be expected though, the former Satedan military man was known for his tenacious fighting abilities as well as his equally tenacious attitude. Loyal to the core, Ronon proved himself time and time again since joining Sheppard's team.

The two matched each other's attacks move for move; the fight might have continued on forever had the voice of Sergeant Harriman not came over the base intercom.

"Teyla, Ronon, to the briefing room immediately."

A slight look of disappointment appeared on both of their faces. This was the only time they had to experience any type of combat. Ronon had been placed on SG-2 at the request of Col. Sheppard but was relieved of his duties after an altercation in a village tavern. His new position was to train incoming airman in different fighting styles. Teyla was assigned to a low echelon SG team that rarely went off world, allowing her to spend as much time with her son as possible.

"I wonder what they want this time. Do you think they have finally reached a decision about returning to Pegasus?" asked Ronon. He and Teyla had begun to gather their gear.

"It would be a great day if that was the case. I am beginning to worry about my people and indeed all the people of our galaxy. The leaders of this world don't see the wraith as an immediate threat; I fear the damage being done by them while we are away. It pains me to not be able to tend to my people," said Teyla with exasperation. "If there is any positive side to this delay it's that I get to spend time with my son."

"How is Torren by the way?"

"He is well; there are many things here on Earth that makes the raising of a child less demanding. Something I have found that calms him down is called a 'Spongebob'. Col. Sheppard introduced him to it and now he seems to enjoy it, I have to say I am growing quite a liking to it myself. Perhaps you should watch it."

"I don't think so. Besides, Teal'c has showed me one of Earth's greatest warriors, a man called Steven Seagal."

"Steven Seagal?"

"Yeah, he's in these things called action movies. He takes on loads of enemies and never loses. Kind of reminds me of someone," said Ronon with a look of self-satisfaction.

The two shared a short laugh before proceeding to the briefing room.

When Sheppard entered the briefing room he was greeted by Col. Abraham Ellis, commander of the _Apollo_.

"Col. Sheppard," said Ellis with a nod.

"Col.," replied Sheppard with a nod of his own.

During his short time on Atlantis, Col. Ellis had managed to make a few enemies; his straight forward, no holds barred attitude and apparent resentment of some of the civilian personnel, specifically Dr. McKay, strongly attributed to this. There was a common joke among the members of the expedition that Col. Stephen Caldwell, commander of the___Daedalus_, was host to a Goa'uld and yet he was better liked than Ellis.

Teyla and Ronon entered the room next. Sheppard shot a friendly glance at Teyla who responded with a gentle smile.

"Where is Dr. McKay?" asked Teyla.

Sheppard glanced around the room as well; he hadn't noticed that his good friend was not present until now.

"Yeah, where is Meredith?" asked Sheppard.

Col. Ellis activated the radio on his ear. "Ellis to _Apollo_, would you please beam down Dr. McKay."

Meredith Rodney McKay, the expedition's foremost expert on Ancient technology, had decided to remain on Atlantis after the city was moved from San Francisco bay to its current location on the moon. He assisted in the continuing repair efforts following the cities battle with the super hive ship.

The bright, white glow of an Asgard transport beam filled the room, when the light faded Dr. McKay was standing in its place.

"This better be important! I will have you know that I was on the verge of another groundbreaking discovery in the ancient database," exclaimed Rodney.

"Right, and by groundbreaking discovery you mean you were with Dr. Keller," said Sheppard.

"Possibly," said Rodney who had begun fidgeting with his hands.

Gen. Landry entered the room from his adjacent office, accompanying him was Col. Caldwell and Dr. Richard Wolsey, the former commander of the Atlantis expedition.

"Well now that we are all here, let's start." said Landry.

Wolsey and Caldwell stood at the monitor on the back wall while everyone else took their seats at the briefing table.

"As you all know, the IOA proposed to the president that the Atlantis expedition be reevaluated," explained Wolsey. "With Atlantis now on Earth they see little reason to exhaust our resources fighting the wraith that, to the best of our knowledge, have no way to reach this galaxy. The president has been reluctant to make any official decision until there is substantial evidence to support either side. The _Daedalus _has returned with a communique from our wraith contact in Pegasus and I believe it is the evidence the president is looking for, although I am not sure which side it favors."

Wolsey turned the floor over to Caldwell who activated the viewing monitor. The image of a familiar friend had appeared, that friend was a wraith named Todd.

Todd, as Col. Sheppard so eloquently named him, was a wraith who had proven his worth as an ally of the expedition. He was the one that had warned of the ZPM powered hive ship and provided Atlantis with the means to travel to Earth. Both he and Sheppard met when they were prisoners of the Genii and developed a mutual friendship, despite the fact that their races were mortal enemies. When Atlantis arrived on Earth, Todd had been in the custody of the United States military before being allowed to return to Pegasus, with some convincing done by Sheppard, to serve as a contact. His communications were usually associated with an impending attack or a great discovery; he never just stops to say hi as Sheppard would say.

The message begun to play as the wraith's dark voice filled the room.

"Greetings, I trust that you have received this message and I regret that I cannot contact you under better circumstances. Word of Atlantis' departure spread quickly among the wraith. When I returned, there was panic among the queens of the various factions, but it was to my surprise the reason of this panic. The wraith have been suffering severe casualties; not at the hands of other hives, nor at the hands of any humans, but from an enemy that I think you are familiar with. I believe you call them the Asgard."

A look of surprise and shock appeared on the faces of Sheppard and his team.

"We have not faced such widespread losses since our war with the Lanteans, not even the replicators inflicted this much damage. We are unaware of how they managed to amass such a sizeable fleet and hide it from our sensors, but they did, and now they are the bane of this galaxy. It seems as if they are searching for something, possibly Atlantis, meaning that they do not know it has left the galaxy. I send you this message not as a distress call for my species but as a warning for yours…"

The message had been abruptly cut short as it appeared the ship Todd was sending the message from came under attack. Several seconds of silence followed the messages end before being broken by Dr. McKay.

"Ok, what the hell was that? Is he serious?"

"We have to assume that he is Dr. McKay," said Caldwell.

"But the Asgard? The last time we saw them they had one ship and they were on the run."

"Well, it appears as if they have more than one ship Rodney," said Sheppard sarcastically.

"What do we know about the Pegasus Asgard?" asked Landry.

"They call themselves the Vanir," explained McKay. "They split from the Asgard we know of over differing scientific and moral opinions. They wanted to experiment on humans to try and solve their cellular degradation, our Asgard did not. This led to them traveling to the Pegasus galaxy to continue their research. With the Wraith and Ancients at war, there was nothing to interfere with their experiments, but when the Ancients lost they were forced to hide from the Wraith. They built mechanical suits to help them survive in the hostile environment of the planet they chose to settle on. There they remained hidden until recently when they breached Atlantis and stole an Ancient device. They were trying to activate the Attero device, but Dr. Jackson and I were able to deactivate it before they could use it. The last we saw of them they were fleeing in their only ship after the other two were destroyed by our traveler friends. If what Todd is saying is true, this is very, very bad. This is the Asgard we are talking about here. We need to do something."

"Not so fast Dr. McKay," interrupted Wolsey. "The IOA has already seen the message and is not completely convinced that what Todd is saying is true. They are aware of the increased tensions placed on the wraith due to the shortened food supply and their inability to reach this galaxy. It is a concern that this is a ploy to have Atlantis return to Pegasus so that the wraith can seize it."

"And what if it's not hmm? What if there is a massive Asgard fleet that could invade this galaxy at any minute, what then?"

"Fortunately Dr. McKay, Gen. O'Neill agrees with you. He is ordering the _Daedalus _and the _Apollo _to return to Pegasus in order to confirm or deny Todd's claims. He has ordered all of you on the mission and you leave in one hour."

"Wait. Why don't we just dial somewhere in Pegasus? Send a team through the gate or at least try and contact someone?" asked Ronon.

"Gee, I wish we would have thought of that," snickered Rodney. "But since the ZPM's were completely depleted when the wormhole drive was activated we have no way to dial Pegasus. Our plan for getting Atlantis back was to drag it behind our ships."

"Regardless of what our plan was we have our orders. I'll be expecting everyone on board my ship twenty minutes prior to departure. Col. Ellis, I'm sure you will expect the same."

"Make that twenty minutes," said Ellis with a hint of pride.

"Well, you all know what to do," said Landry. " Dismissed."

With that, the mad scramble had begun. Ellis and Caldwell returned to their respective ships to prepare their crews for the mission. McKay returned to Atlantis to gather his research equipment and was beamed directly to the ___Daedalus_; he did not want to spend several days with Ellis on the ___Apollo_. Teyla made arrangements for her son to be taken of and Ronon gathered his equipment. When the time came they all met on the bridge of the ___Daedalus _and prepared to depart.

Caldwell contacted the ___Apollo _and received the good to go signal from Ellis.

"Ok here we go. Engage hyper-drive on my mark. Three, two, one…"

Before Caldwell could give the command, the helmsman was alerted to the activation of two hyperspace windows above Earth.

"We have contacts," alerted the helmsman.

"What is it?"

"Two unidentified objects sir. Too small to be ships. They're headed for the moon sir"

"Shields up," ordered Caldwell. "Bring rail guns on line"

"Shields up Col. Weapons are online."

"Alert Atlantis that they have company and plot an intercept course."

"Our transmissions are being jammed Colonel. The objects are moving too fast, we won't be able them reach them in time."

"Is the city cloaked?"

"No sir."

"Caldwell to _Apollo__, _can you..."

Again the colonel was interrupted, this time by the bright flashing light that enveloped Atlantis. It remained constant for several seconds before finally disappearing.

Caldwell abruptly stood up from his chair and approached the large viewing window.

"What the hell just happened."

"Atlantis, it's gone sir."

There was a mad scramble of SGC personnel following the disappearance of Atlantis.

How could that have happened? Why had the cities deep space sensors not detected the beam satellites in hyperspace? These were the questions every researcher in the SGC attempted to answer as Gen. Landry met with Col. Caldwell and company in the briefing room.

"Can someone explain me to what the hell just happened?"

McKay took it upon himself to answer Landry's question. "Atlantis was beamed out of this galaxy by the Vanir, right under our nose."

"Now wait a minute Dr. McKay, we have no proof that this was the Asgard," said Caldwell.

"Oh, right it must have been the Nox," said McKay sarcastically. "How many other races do we know that could beam an entire city?"

"What makes you so sure that it was the Vanir?" asked Landry.

"Look, the technology was very similar to our own beaming technology. The readings were almost identical."

"It did look like an Asgard beam sir," added Sheppard.

"So if we are assuming it was these rouge Asgard, the next question is why. Why would they take Atlantis?" asked Caldwell.

"Gee I don't know, maybe it's because of the cities excellent dining facilities," snickered McKay.

"Rodney!" snapped Sheppard.

"I'm sorry if I'm coming off as a jerk but every second I sit here explaining the obvious is another second Atlantis is in the hands of the Vanir. To give everyone a recap, the Vanir suffer from the same cellular degeneration as our Asgard did. The difference being that they were able to make significant advances in their research due to experimentation on humans. This has slowed down their disease but not cured it. They probably think that there is something in the Ancient database that can help them, not to mention all the other technologies the city possesses."

"Do we have any idea where the city is now?" asked Landry.

"We can't know for sure right now, but I can take one good guess as where it was taken." said McKay.

"Can't we just dial the cities stargate?" asked Sheppard.

"If only it was that simple. We had to disable the Atlantis stargate because while it was on Earth it took precedence over our own gate. Besides, we don't have a ZPM anyway."

"Well regardless, we still have dozens of research personnel on board along with several security teams. This is rescue mission as much as a recovery one sir," said Sheppard.

"I agree, that's why we need to act fast," said Landry. "Col. Caldwell, are the _Daedalus _and _Apollo _still ready to go?"

"Yes sir."

"I am ordering additional military personnel and supplies to be added to the mission. Although it appears as if the our original question regarding the Vanir have been answered, I am still recommending that you gather as much intel as you can. I'm sure the Pegasus alpha site can serve as a base of operations for now. If possible, find our wraith friend and see what he knows. Good luck and godspeed, dismissed."

* * *

When Todd awoke, it was clear that he was no longer on board his hive ship. A wraith hive ship had a very distinct smell, it was organic after all, and the scent of machines that filled the air was the furthest from it.

The last thing he remembered was being on his ship. He had been recording a message for the humans, warning them of the galaxies newest cancer. The ship had been attacked before he could finish, the message had barely been sent before communications failed. Weapons had been knocked out almost immediately; the enemy knew exactly where to fire. The same teleportation technology the humans possessed was being used by the enemy to board the hive; the signal could not be jammed. Amidst the exploding power conduits and venting steam veins, Todd had gotten a small glimpse of what hunted them. Never before had he seen anything like it, not even during the war with the Ancients. Beings completely encased in metal suits marched on the bridge, they had begun to fire weapons on his crew. Todd had been struck in the back by one of these weapons, causing him to full unconscious onto the cold floor of the hive ship. Next thing he knew he had awoken here, wherever here was.

Todd had begun to regain his composure, sitting upright against the back wall of the room he had found himself him. Being held captive was nothing new to him but it was different this time, he felt different. It became clear to him what the difference was after he tried to reach out with his mind to feel for other wraith nearby only to be met with a searing pain in his head. A circular device had been placed on his left temple that was inhibiting his psychic abilities.

Todd was sitting against the wall of his cell when something unexpected happened, the device suddenly fell off of his head. His senses slowly started to come back to him. Just as his vision was beginning to clear an explosion ripped the cell door apart. The sudden sensory overload took its toll on Todd who was now curled into a makeshift ball in the back of the cell trying to protect his head and chest from any debris or weapons fire. He hadn't fed in quite some time so his regeneration powers were weak, he could not afford to be harmed.

He slowly got to his feet and was met with a surprise. Standing in the newly opened doorway of his cell was what appeared to be a human. There was something different about this human though, Todd could smell it.

"Have you come to kill me?" asked Todd.

"No, I've come to rescue you," said the human.

"Rescue me? Not that I am not grateful for the effort but I might ask who you are."

The human stepped forward into the cell, his face no longer hidden by the bright lights of the hallway outside of the cell. He was indeed human, his skin was of a much darker tone then that of Sheppard. He looked different than most other humans Todd has seen, something felt very familiar about this particular human; almost as if he and the mysterious man had something in common.

"The names Ford and we don't have much time."


End file.
